Users of Tor hidden services report that their copies of "Tor Browser" (a modified, locked-down version of Firefox that uses Tor by default) were infected with malicious Javascript that de-anonymized them, and speculate that this may have originated with with FBI. Tor Browser formerly came with Javascript disabled by default, but it was switched back on again recently to make the browser more generally useful.

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Note: This applies to Tor Browser Bundle and Tails Iceweasel (Firefox derivative browser) and any other browsers with Javascript turned on by default.